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基于第一性原理研究脱硫杆菌导电菌毛肽亚基的分子和电子结构。

Molecular and electronic structure of the peptide subunit of Geobacter sulfurreducens conductive pili from first principles.

机构信息

Departamento de Física dos Materiais e Mecânica, Instituto de Física, Universidade de São Paulo , SP, Brazil.

出版信息

J Phys Chem A. 2012 Aug 2;116(30):8023-30. doi: 10.1021/jp302232p. Epub 2012 Jul 23.

Abstract

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved α-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pilin was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's α-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

摘要

细菌 Geobacter sulfurreducens 通过呼吸金属氧化物需要将一种小肽(GS 菌毛蛋白)组装成称为菌毛的导电丝。我们通过开发同源模型并对菌毛肽在真空中和溶液中的分子动力学模拟,深入了解了 GS 菌毛蛋白对菌毛导电性的贡献。结果与一个主要呈螺旋状的肽一致,该肽含有菌毛组装所需的保守α-螺旋区,但带有较短的羧基末端无规卷曲片段,而不是其他细菌菌毛的大球形头部。还从第一性原理探索了菌毛的电子结构,结果表明,即使在潮湿的环境中,菌毛也具有分相的电荷分布和较低的电子 HOMO-LUMO 能隙。低电子能带隙是由菌毛的α-螺旋中肽键偶极的排列以及溶液中的离子和蛋白质中的氨基酸所产生的强静电场引起的。电子结构还揭示了菌毛中含有芳香族氨基酸的区域和 HOMO 和 LUMO 状态存在的高共振空间区域中的轨道离域的某种程度,这可以为电子在热涨落下的跳跃提供最佳环境。因此,这些研究中揭示的菌毛的结构和电子特征支持了菌毛肽环境优化电子传导的观点。

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